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Background: Spinach downy mildew, caused by the obligate oomycete pathogen, Peronospora effusa remains a major concern for spinach production. Disease control is predominantly based on development of resistant spinach cultivars. However, new races and novel isolates of the pathogen continue to emerge and overcome cultivar resistance. Currently there are 20 known races of P. effusa. Here we characterized the transcriptomes of spinach, Spinacia oleracea, and P. effusa during disease progression using the spinach cultivar Viroflay, the near isogenic lines NIL1 and NIL3, and P. effusa races, R13 and R19, at 24 h post inoculation and 6 days post inoculation. A total of 54 samples were collected and subjected to sequencing and transcriptomic analysis., Results: Differentially expressed gene (DEG) analysis in resistant spinach interactions of R13-NIL1 and R19-NIL3 revealed spinach DEGs from protein kinase-like and P-loop containing families, which have roles in plant defense. The homologous plant defense genes included but were not limited to, receptor-like protein kinases (Spiol0281C06495, Spiol06Chr21559 and Spiol06Chr24027), a BAK1 homolog (Spiol0223C05961), genes with leucine rich repeat motifs (Spiol04Chr08771, Spiol04Chr01972, Spiol05Chr26812, Spiol04Chr11049, Spiol0084S08137, Spiol03Chr20299) and ABC-transporters (Spiol02Chr28975, Spiol06Chr22112, Spiol06Chr03998 and Spiol04Chr09723). Additionally, analysis of the expression of eight homologous to previously reported downy mildew resistance genes revealed that some are differentially expressed during resistant reactions but not during susceptible reactions. Examination of P. effusa gene expression during infection of susceptible cultivars identified expressed genes present in R19 or R13 including predicted RxLR and Crinkler effector genes that may be responsible for race-specific virulence on NIL1 or NIL3 spinach hosts, respectively., Conclusions: These findings deliver foundational insight to gene expression in both spinach and P. effusa during susceptible and resistant interactions and provide a library of candidate genes for further exploration and functional analysis. Such resources will be beneficial to spinach breeding efforts for disease resistance in addition to better understanding the virulence mechanisms of this obligate pathogen., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Four isolates of Neofusicoccum parvum , collected from diseased hemp ( Cannabis sativa ) plants over a period of 2 years and shown to be pathogenic on C. sativa, were examined in this study. Their genome sizes ranged between 42.8 and 44.4 Mb, with 16,499 ± 72 predicted genes across the four isolates., Competing Interests: The authors declare no conflict of interest.

Spinach downy mildew, caused by the obligate oomycete pathogen Peronospora effusa , is a worldwide constraint on spinach production. The role of airborne sporangia in the disease cycle of P. effusa is well established, but the role of the sexual oospores in the epidemiology of P. effusa is less clear and has been a major challenge to examine experimentally. To evaluate seed transmission of spinach downy mildew via oospores in this study, isolated glass chambers were employed in two independent experiments to grow out oospore-infested spinach seed and noninfested seeds mixed with oospore-infested crop debris. Downy mildew diseased spinach plants were observed 37 and 34 days after planting in the two isolator experiments, respectively, in the chambers that contained one of two oospore-infested seed lots or seeds coated with oospore-infested leaves. Spinach plants in isolated glass chambers initiated from seeds without oospores did not show downy mildew symptoms. Similar findings were obtained using the same seed lot samples in a third experiment conducted in a growth chamber. In direct grow out tests to examine oospore infection on seedlings performed in a containment greenhouse with oospore-infested seed of two different cultivars, characteristic Peronospora sporangiophores were observed growing from a seedling of each cultivar. The frequency of seedlings developing symptoms from 82 of these oospore-infested seed indicated that approximately 2.4% of seedlings from infested seed developed symptoms, and 0.55% of seedlings from total seeds assayed developed symptoms. The results provide evidence that oospores can serve as a source of inoculum for downy mildew and provide further evidence of direct seed transmission of the downy mildew pathogen to seedlings in spinach via seedborne oospores., Competing Interests: The author(s) declare no conflict of interest.

There is a recent unparalleled increase in demand for rice in sub-Saharan Africa, yet its production is affected by blast disease. Characterization of blast resistance in adapted African rice cultivars can provide important information to guide growers and rice breeders. We used molecular markers for known blast resistance genes ( Pi genes; n = 21) to group African rice genotypes ( n = 240) into similarity clusters. We then used greenhouse-based assays to challenge representative rice genotypes ( n = 56) with African isolates ( n = 8) of Magnaporthe oryzae which varied in virulence and genetic lineage. The markers grouped rice cultivars into five blast resistance clusters (BRC) which differed in foliar disease severity. Using stepwise regression, we found that the Pi genes associated with reduced blast severity were Pi50 and Pi65, whereas Pik-p, Piz-t, and Pik were associated with increased susceptibility. All rice genotypes in the most resistant cluster, BRC 4, possessed Pi50 and Pi65 , the only genes that were significantly associated with reduced foliar blast severity. Cultivar IRAT109, which contains Piz-t , was resistant against seven African M. oryzae isolates, whereas ARICA 17 was susceptible to eight isolates. The popular Basmati 217 and Basmati 370 were among the most susceptible genotypes. These findings indicate that most tested genes were not effective against African blast pathogen collections. Pyramiding genes in the Pi2/9 multifamily blast resistance cluster on chromosome 6 and Pi65 on chromosome 11 could confer broad-spectrum resistance capabilities. To gain further insights into genomic regions associated with blast resistance, gene mapping could be conducted with resident blast pathogen collections. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license., Competing Interests: The author(s) declare no conflict of interest.

Commercial production of spinach ( Spinacia oleracea L.) is centered in California and Arizona in the US, where downy mildew caused by Peronospora effusa is the most destructive disease. Nineteen typical races of P. effusa have been reported to infect spinach, with 16 identified after 1990. The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach. We attempted to map and delineate the RPF2 locus at a finer resolution, identify linked single nucleotide polymorphism (SNP) markers, and report candidate downy mildew resistance ( R ) genes. Progeny populations segregating for RPF2 locus derived from resistant differential cultivar Lazio were infected using race 5 of P. effusa and were used to study for genetic transmission and mapping analysis in this study. Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb of chromosome 3 with peak SNP (Chr3_1, 221, 009) showing a LOD value of 61.6 in the GLM model in TASSEL, which was within 1.08 Kb from Spo12821, a gene that encodes CC-NBS-LRR plant disease resistance protein. In addition, a combined analysis of progeny panels of Lazio and Whale segregating for RPF2 and RPF3 loci delineated the resistance section in chromosome 3 between 1.18-1.23 and 1.75-1.76 Mb. This study provides valuable information on the RPF2 resistance region in the spinach cultivar Lazio compared to RPF3 loci in the cultivar Whale. The RPF2 and RPF3 specific SNP markers, plus the resistant genes reported here, could add value to breeding efforts to develop downy mildew resistant cultivars in the future., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© The Author(s) 2023. Published by Oxford University Press.)

Spinach ( Spinacia oleracea ) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci ( RPF3 ) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the  RPF3  locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bhattarai, Olaoye, Mou, Correll and Shi.)

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete Peronospora effusa . In the past two decades, new pathogen races have repeatedly overcome the resistance used in newly released cultivars, urging the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew pathogens and are effective against some pathogen races/isolates. This work aimed to evaluate the worldwide USDA spinach germplasm collections and commercial cultivars for resistance to downy mildew pathogen in the field condition under natural inoculum pressure and conduct genome wide association analysis (GWAS) to identify resistance-associated genomic regions (alleles). Another objective was to evaluate the prediction accuracy (PA) using several genomic prediction (GP) methods to assess the potential implementation of genomic selection (GS) to improve spinach breeding for resistance to downy mildew pathogen. More than four hundred diverse spinach genotypes comprising USDA germplasm accessions and commercial cultivars were evaluated for resistance to downy mildew pathogen between 2017-2019 in Salinas Valley, California and Yuma, Arizona. GWAS was performed using single nucleotide polymorphism (SNP) markers identified via whole genome resequencing (WGR) in GAPIT and TASSEL programs; detected 14, 12, 5, and 10 significantly associated SNP markers with the resistance from four tested environments, respectively; and the QTL alleles were detected at the previously reported region of chromosome 3 in three of the four experiments. In parallel, PA was assessed using six GP models and seven unique marker datasets for field resistance to downy mildew pathogen across four tested environments. The results suggest the suitability of GS to improve field resistance to downy mildew pathogen. The QTL, SNP markers, and PA estimates provide new information in spinach breeding to select resistant plants and breeding lines through marker-assisted selection (MAS) and GS, eventually helping to accumulate beneficial alleles for durable disease resistance., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nanjing Agricultural University.)

Downy mildew of spinach, caused by Peronospora effusa , is a major economic threat to both organic and conventional spinach production. Symptomatic spinach leaves are unmarketable and spinach with latent infections are problematic because symptoms can develop postharvest. Therefore, early detection methods for P. effusa could help producers identify infection before visible symptoms appear. Recombinase polymerase amplification (RPA) provides sensitive and specific detection of pathogen DNA and is a rapid, field-applicable method that does not require advanced technical knowledge or equipment-heavy DNA extraction. Here, we used comparative genomics to identify a unique region of the P. effusa mitochondrial genome to develop an RPA assay for the early detection of P. effusa in spinach leaves. In tandem, we established a TaqMan quantitative PCR (qPCR) assay and used this assay to validate the P. effusa specificity of the locus across Peronospora spp. and to compare assay performance. Neither the TaqMan qPCR nor the RPA showed cross reactivity with the closely related beet downy mildew pathogen, P. schachtii . TaqMan qPCR and RPA have detection thresholds of 100 and 900 fg of DNA, respectively. Both assays could detect P. effusa in presymptomatic leaves, with RPA-based detection occurring as early as 5 days before the appearance of symptoms and TaqMan qPCR-based detection occurring after 24 h of plant exposure to airborne spores. Implementation of the RPA detection method could provide real-time information for point-of-care management strategies at field sites.

Downy mildew disease of spinach, caused by the oomycete Peronospora effusa , causes major losses to spinach production. In this study, the 17 chromosomes of P. effusa were assembled telomere-to-telomere, using Pacific Biosciences high-fidelity reads. Of these, 16 chromosomes are complete and gapless; chromosome 15 contains one gap bridging the nucleolus organizer region. This is the first telomere-to-telomere genome assembly for an oomycete. Putative centromeric regions were identified on all chromosomes. This new assembly enables a reevaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora species. Genome fragments consistently underrepresented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. Putative effectors were annotated on 16 of the 17 chromosomes. The intergenic distances between annotated genes were consistent with compartmentalization of the genome into gene-dense and gene-sparse regions. Genes encoding putative effectors were enriched in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae ; high levels of synteny were also detected with Phytophthora sojae . Extensive synteny between phylogenetically distant species suggests that many other oomycete species may have similar chromosome organization. Therefore, this assembly provides the foundation for genomic analyses of diverse oomycetes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers ( n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae , and brown spot, Cochliobolus miyabeanus , on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae , in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.

White rust, caused by Albugo occidentalis , is one of the major yield-limiting diseases of spinach ( Spinacia oleracea ) in some major commercial production areas, particularly in southern Texas in the United States. The use of host resistance is the most economical and environment-friendly approach to managing white rust in spinach production. The objectives of this study were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction accuracy (PA). A GWAS panel of 346 USDA (US Dept. of Agriculture) germplasm accessions was phenotyped for white rust resistance under field conditions and GWAS was performed using 13 235 whole-genome resequencing (WGR) generated SNPs. Nine SNPs, chr2_53 049 132, chr3_58 479 501, chr3_95 114 909, chr4_9 176 069, chr4_17 807 168, chr4_83 938 338, chr4_87 601 768, chr6_1 877 096, and chr6_31 287 118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four scenarios were tested for PA using Pearson's correlation coefficient (r) between the genomic estimation breeding value (GEBV) and the observed values: (1) different ratios between the training set and testing set (fold), (2) different GP models, (3) different SNP numbers in three different SNP sets, and (4) the use of GWAS-derived significant SNP markers. The results indicated that a 2- to 10-fold difference in the various GP models had similar, although not identical, averaged r values in each SNP set; using GWAS-derived significant SNP markers would increase PA with a high r-value up to 0.84. The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS)., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nanjing Agricultural University.)

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae , represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Background: Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16., Results: Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69-11.28 Kb of the peak SNP., Conclusions: Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

Key Message: The Fs gene, which controls spinach fruit spines, was fine mapped to a 0.27 Mb interval encompassing four genes on chromosome 3. There are two types of fruit of spinach (Spinacia oleracea L.), spiny and spineless, which are visually distinguishable by the spines of fruit coat. In spinach breeding, the fruit characteristic is an important agronomic trait that have impacts on "seed" treatment and mechanized sowing. However, the gene(s) controlling the fruit spiny trait have not been characterized and the genetic mechanism of this trait remained unclear. The objectives of the study were to fine map the gene controlling fruit spines and develop molecular markers for marker-assisted selection purpose. Genetic analysis of the spiny trait in segregating populations indicated that fruit spines were controlled by a single dominant gene, designated as Fs. Using a super-BSA method and recombinants analysis in a BC 1 population, Fs was mapped to a 1.9-Mb interval on chromosome 3. The Fs gene was further mapped to a 0.27-Mb interval using a recombinant inbred line (RIL) population with 120 lines. From this 0.27 Mb region, four candidate genes were identified in the reference genome. The structure and expression of the four genes were compared between the spiny and spineless parents. A co-dominant marker YC-15 was found to be co-segregating with the fruit spines trait, which produced a 129-bp fragment specific to spiny trait and a 108-bp fragment for spineless fruit. This marker can predict spiny trait with a 94.8% accuracy rate when tested with 100 diverse germplasm, suggesting that this marker would be valuable for marker-assisted selection in spinach breeding.

Background: Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus., Results: Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes., Conclusion: Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen.

Leaf curl of celery, caused by Colletotrichum acutatum sensu lato, has been reported in the United States. A multilocus phylogenetic analysis with three genes was conducted with a collection of isolates from celery ( n = 23) and noncelery ( n = 29) hosts to evaluate their taxonomic position within C. acutatum sensu lato. The three DNA regions used for phylogenetic analysis included the introns of the glutamine synthase GS and glyceraldehyde-3-phosphate dehydrogenase GPDH genes, and the partial sequence of the histone3 his3 gene. Moreover, celery and noncelery isolates were evaluated for vegetative compatibility and pathogenicity on celery. Culture filtrates from celery and noncelery isolates were also evaluated for their ability to reproduce leaf curl symptoms. A total of 23 celery isolates were evaluated based on phylogenetic analysis, which showed that all celery isolates were closely related and belonged to the newly described species C. fioriniae . The celery isolates were grouped into six vegetative compatibility groups, indicating that the population was not clonal. Isolates of C. fioriniae from celery (22 of 23) and other hosts (26 of 29) caused leaf curl symptoms. Isolates of C. acutatum , C. nymphaeae , and C. godetiae were pathogenic but did not cause leaf curl symptoms. Isolates of C. lupini , C. johnstonii , and C. gloeosporioides were not pathogenic on celery. In addition, cell-free fungal culture filtrates caused leaf curl symptoms on celery, indicating that certain isolates produce a metabolite that can cause leaf curl symptoms on celery, possibly indole acetic acid.

Leaf spot diseases of spinach, caused by Colletotrichum spinaciae , has become a major production constraint in several production areas, including Texas, in recent years. Leaf spot symptoms were observed in several fields in Texas in 2016 and 2017, with typical anthracnose-like symptoms and leaves with small, circular, and sunken lesions that appeared similar to injury from windblown sand. The lesions were plated on potato dextrose agar, from which fungal cultures were recovered. The fungi were identified based on morphology and sequence analysis of the introns of glutamate synthetase and glyceraldehyde-3-phosphate dehydrogenase (for isolates determined to be Colletotrichum spp.) and the internal transcribed spacer ribosomal DNA (for isolates determined to be Myrothecium spp.). Based on foliar symptoms, fungal colony and spore morphology, pathogenicity tests of fungal isolates on the spinach cultivar 'Viroflay', and DNA sequence analysis of the isolates, the symptoms on spinach leaves for two sets of samples were caused by Colletotrichum coccodes and Colletotrichum truncatum , and leaf spots resembling damage from windblown sand were caused by Myrothecium verrucaria . This is the first report of spinach leaf spot diseases caused by C. coccodes , C. truncatum , and M. verrucaria in the United States. C. coccodes and C. truncatum caused severe symptoms on the spinach cultivar 'Viroflay', whereas M. verrucaria caused symptoms of intermediate severity. Fungicide efficacy tests demonstrated that chlorothalonil, mancozeb, pyraclostrobin, fluxapyroxad + pyraclostrobin, and penthiopyrad were completely effective at preventing leaf spots caused by any of these pathogens when applied 24 h before inoculation of 'Viroflay' plants in greenhouse trials.

Downy mildew, caused by the oomycete Peronospora effusa , is the most economically important disease on spinach. Fourteen new races of P. effusa have been identified in the last three decades. The frequent emergence of new races of P. effusa continually overcome the genetic resistance to the pathogen. The objectives of this research were to more clearly map the downy mildew resistance locus RPF 1 in spinach, to identify single nucleotide polymorphism (SNP) markers associated with the resistance, and to refine the candidate genes responsible for the resistance. Progeny from populations generated from crosses of cultivars resistant (due to RPF 1) to race 13 of P. effusa (Swan, T-Bird, Squirrel, and Tonga) with race 13 susceptible cultivars (Whale and Polka) were inoculated and the downy mildew disease response determined. Association analysis was performed in TASSEL, GAPIT, PLINK, and GENESIS programs using SNP markers identified from genotyping by sequencing (GBS). Association analysis mapped the race 13 resistance loci ( RPF 1) to positions 0.39, 0.69, 0.94-0.98, and 1.2 Mb of chromosome 3. The associated SNPs were within 1-7 kb of the disease resistance genes Spo12784, Spo12719, Spo12905, and Spo12821, and 11-18 Kb from Spo12903. This study extended our understanding of the genetic basis of downy mildew resistance in spinach and provided the most promising candidate genes Spo12784 and Spo12903 near the RPF 1 locus, to pursue functional validation. The SNP markers may be used to select for the resistant lines to improve genetic resistance against the downy mildew pathogen and in developing durably resistant cultivars., (Copyright © 2020 Bhattarai, Shi, Feng, Dhillon, Mou and Correll.)

Downy mildew of spinach, caused by the obligate pathogen Peronospora effusa , remains the most important constraint in the major spinach production areas in the United States. This disease can potentially be initiated by asexual sporangiospores via "green bridges", sexually derived oospores from seed or soil, or dormant mycelium. However, the relative importance of the various types of primary inoculum is not well known. The ability of P. effusa sporangiospores to withstand abiotic stress, such as desiccation, and remain viable during short- and long-distance dispersal and the ability of oospores to germinate and infect seedlings remain unclear. Thus, the primary objectives of this research were to evaluate the impact of desiccation on sporangiospore survival and infection efficiency and examine occurrence, production, and germination of oospores. Results indicate that desiccation significantly reduces sporangiospore viability as well as infection potential. Leaf wetness duration of 4 h was needed for disease establishment by spinach downy mildew sporangiospores. Oospores were observed in leaves of numerous commercial spinach cultivars grown in California in 2018 and Arizona in 2019. Frequency of occurrence varied between the two states-years. The presence of opposite mating types in spinach production areas in the United States was demonstrated by pairing isolates in controlled crosses and producing oospores on detached leaves as well as intact plants. Information from the study of variables that affect sporangiospore viability and oospore production will help in improving our understanding of the epidemiology of this important pathogen, which has implications for management of spinach downy mildew.

Leaf spot diseases have become a major concern in spinach production in the United States. Determining the causal agents of leaf spots on spinach, their prevalence and pathogenicity, and fungicide efficacy against these pathogens is vital for effective disease management. Spinach leaves with leaf spots were collected from Texas, California, Arizona, and South Carolina from 2016 to 2018, incubated in a moist chamber, and plated on potato dextrose and tryptic soy agar media. Fungal and bacterial colonies recovered were identified based on morphology and sequence analysis of the internal transcribed spacer rDNA and 16S rRNA, respectively. Two predominant genera were isolated: (i) Colletotrichum spp., which were identified to species based on sequences of both introns of the glutamate synthetase ( GS -I) and glyceraldehyde-3-phosphate dehydrogenase ( gapdh -I) genes; and (ii) Stemphylium spp., identified to species based on sequences of the gapdh and calmodulin ( cmdA ) genes. Anthracnose ( Colletotrichum spinaciae ) and Stemphylium leaf spot ( Stemphylium vesicarium and S. beticola ) were the predominant diseases. Additional fungi recovered at very limited frequencies that were also pathogenic to spinach included Colletotrichum coccodes , C. truncatum , Cercospora beticola , and Myrothecium verrucaria . All of the bacterial isolates were not pathogenic on spinach. Pathogenicity tests showed that C. spinaciae , S. vesicarium , and S. beticola caused significant leaf damage. The fungicides Bravo WeatherStik (chlorothalonil), Dithane F-45 (mancozeb), Cabrio (pyraclostrobin), and Merivon (fluxapyroxad and pyraclostrobin) were highly effective at reducing leaf spot severity caused by an isolate of each of C. spinaciae and S. vesicarium , when inoculated individually and in combination.

Key Message: A SLAF-BSA approach was used to locate the RPF1 locus. The three most likely candidate genes were identified which provide a basic for cloning the resistance gene at the RPF1 locus. Spinach downy mildew is a globally devastating oomycete disease. The use of downy mildew resistance genes constitutes the most effective approach for disease management. Hence, the objective of the present study was to fine map the first-reported resistance locus RPF1. The resistance allele at this resistance locus was effective against races 1-7, 9, 11, 13, and 15 of Peronospora farinosa f. sp. spinaciae (P. effusa). The approach fine mapped RPF1 using specific-locus amplified fragment sequencing (SLAF-Seq) technology combined with bulked segregant analysis. A 1.72 Mb region localized on chromosome 3 was found to contain RPF1 based on association analysis. After screening recombinants with the SLAF markers within the region, the region was narrowed down to 0.89 Mb. Within this region, 14 R genes were identified based on the annotation information. To identify the genes involved in resistance, resequencing of two resistant inbred lines (12S2 and 12S3) and three susceptible inbred lines (12S1, 12S4, and 10S2) was performed. The three most likely candidate genes were identified via amino acid sequence analysis and conserved domain analysis between resistant and susceptible inbred lines. These included Spo12729, encoding a receptor-like protein, and Spo12784 and Spo12903, encoding a nucleotide-binding site and leucine-rich repeat domains. Additionally, based on the sequence variation in the three genes between the resistant and susceptible lines, molecular markers were developed for marker-assisted selection. The results could be valuable in cloning the RPF1 alleles and improving our understanding of the interaction between the host and pathogen.

Downy mildew disease, caused by the obligate oomycete pathogen Peronospora effusa, is the most important economic constraint for spinach production. Three races (races 12, 13, and 14) of P. effusa have been sequenced and assembled. The draft genomes of these three races have been deposited to GenBank and provide useful resources for dissecting the interaction between the host and the pathogen and may provide a framework for determining the mechanism by which new races of the pathogen are rapidly emerging.

Downy mildew disease, caused by Peronospora effusa (=P. farinosa f. sp. spinaciae [Pfs]), is the most economically important disease of spinach. Current high-density fresh-market spinach production provides conducive conditions for disease development, and downy mildew frequently forces growers to harvest early owing to disease development, to cull symptomatic leaves prior to harvest, or to abandon the field if the disease is too severe. The use of resistant cultivars to manage downy mildew, particularly on increasing acreages of organic spinach production, applies strong selection pressure on the pathogen, and many new races of Pfs have been identified in recent years in spinach production areas worldwide. To monitor the virulence diversity in the Pfs population, downy mildew samples were collected from spinach production areas and tested for race identification based on the disease reactions of a standard set of international spinach differentials. Two new races (designated races 15 and 16) and eight novel strains were identified between 2013 and 2017. The disease reaction of Pfs 15 was similar to race 4, except race 4 could not overcome the resistance imparted by the RPF9 locus. Several resistance loci (RPF1, 2, 4, and 6) were effective in preventing disease caused by Pfs 15. The race Pfs 16 could overcome several resistance loci (RPF2, 4, 5, 9, and 10) but not others (RPF1, 3, 6, and 7). One novel strain (UA1014) could overcome the resistance of spinach resistant loci RPF1 to RPF7 but only infected the cotyledons and not the true leaves of certain cultivars. A new set of near-isogenic lines has been developed and evaluated for disease reactions to the new races and novel strains as differentials. None of the 360 U.S. Department of Agriculture spinach germplasm accessions tested were resistant to Pfs 16 or UA1014. A survey of isolates over several years highlighted the dynamic nature of the virulence diversity of the Pfs population. Identification of virulence diversity and evaluation of the genetics of resistance to Pfs will continue to allow for a more effective disease management strategy through resistance gene deployment.

A unique foliar disease of spinach, determined to be caused by Pythium aphanidermatum, was observed on spinach in Yuma County, AZ and Imperial County, CA desert spinach production areas in both 2015 and 2016. The foliar symptoms of the disease included water-soaked foliage, rapid collapse of young plants, and white, aerial, cottony mycelia. The disease was associated with hot (27 to 42°C) and wet conditions associated with overhead irrigation under high-density plantings (>8.0 million seeds/ha). Isolations were performed on symptomatic tissue, and DNA was recovered from pure culture of the isolates recovered and sequenced using the internal transcribed spacer (ITS) ribosomal DNA (rDNA) primers ITS1/ITS4 and gene cytochrome oxidase I (COXI) primers FM55 and FM59. BLAST searches in GenBank indicated that the isolates were P. aphanidermatum based on 99 to 100% homology of ITS rDNA. Moreover, the DNA sequences of the ITS and COXI were identical for the five representative isolates. The objective of this research was to determine whether P. aphanidermatum recovered from symptomatic spinach tissue was able to cause foliar web blight and damping-off of spinach and other crops. In addition to spinach, other hosts evaluated included cotton, soybean, pepper, tomato, cucumber, melon, squash, lettuce, corn, wheat, and rice in greenhouse trials. Inoculations were performed by either foliar inoculations or infesting the soil with plugs of potato dextrose agar colonized by the P. aphanidermatum. Web blight symptoms were severe on spinach and all other dicotyledonous hosts tested, except lettuce. No web blight symptoms were observed on corn or rice, and only minor symptoms were observed on 10-day-old seedlings of wheat. P. aphanidermatum caused severe preemergence damping-off of all dicotyledonous plant species tested but only caused limited seedling size reduction in corn and wheat. Mefenoxam treatment of spinach seed provided complete protection against preemergence damping-off of spinach at both low (0.15 g a.i./kg of seed) and high (0.70 g a.i./kg of seed) rates of application, and the high rate of the application resulted in complete protection against web blight of spinach for 10 to 20 days after planting.

Background: Rice blast, caused by the ascomycete Magnaporthe oryzae (Mo), imposes a major constraint on rice productivity. Managing the disease through the deployment of host resistance requires a close understanding of race structure of the pathogen population., Results: The host/pathogen interaction between isolates sampled from four Mo populations collected across the rice-producing regions of China was tested using two established panels of differential cultivars. The clearest picture was obtained from the Chinese cultivar panel, for which the frequency of the various races, the race diversity index, the specific race isolate frequency, and the frequency of the three predominant races gave a consistent result, from which it was concluded that the pathogen population present in the southern production region was more diverse than that in the northeastern region. The four blast resistance genes Pi1, Pik, Pik-m, and Piz all still remain effective in the southern China rice production area, as does Pi1 in the northeastern region. The effectiveness of Pita, Pik-p, Piz, and Pib is restricted to single provinces. The distinctive resistance profile shown by the Chinese differential cultivar set implied the presence of at least five as yet unidentified blast resistance genes., Conclusions: The Chinese differential cultivar set proved to be more informative than the Japanese one for characterizing the race structure of the rice blast pathogen in China. A number of well characterized host resistance genes, in addition to some as yet uncharacterized ones, remain effective across the major rice production regions in China.

A collection of 122 isolates of Magnaporthe oryzae, from nine sub-Saharan African countries, was assessed for virulence diversity and genetic relatedness. The virulence spectrum was assessed by pathotype analysis with a panel of 43 rice genotypes consisting of differential lines carrying 24 blast resistance genes (R-genes), contemporary African rice cultivars, and susceptible checks. The virulence spectrum among isolates ranged from 5 to 80%. Five isolates were avirulent to the entire rice panel, while two isolates were virulent to ∼75% of the panel. Overall, cultivar 75-1-127, the Pi9 R-gene donor, was resistant to all isolates (100%), followed by four African rice cultivars (AR105, NERICA 15, 96%; NERICA 4, 91%; and F6-36, 90%). Genetic relatedness of isolates was assessed by single nucleotide polymorphisms derived from genotyping-by-sequencing and by vegetative compatibility tests. Phylogenetic analysis of SNPs of a subset of isolates (n = 78) revealed seven distinct clades that differed in virulence. Principal component analysis showed isolates from East Africa were genetically distinct from those from West Africa. Vegetative compatibility tests of a subset of isolates (n = 65) showed no common groups among countries. This study shows that blast disease could be controlled by pyramiding of Pi9 together with other promising R-genes into rice cultivars that are adapted to East and West African regions.

Aims: To develop multiplex TaqMan real-time PCR assays for detection of spinach seedborne pathogens that cause economically important diseases on spinach., Methods and Results: Primers and probes were designed from conserved sequences of the internal transcribed spacer (for Peronospora farinosa f. sp. spinaciae and Stemphylium botryosum), the intergenic spacer (for Verticillium dahliae) and the elongation factor 1 alpha (for Cladosporium variabile) regions of DNA. The TaqMan assays were tested on DNA extracted from numerous isolates of the four target pathogens, as well as a wide range of nontarget, related fungi or oomycetes and numerous saprophytes commonly found on spinach seed. Multiplex real-time PCR assays were evaluated by detecting two or three target pathogens simultaneously. Singular and multiplex real-time PCR assays were also applied to DNA extracted from bulked seed and single spinach seed., Conclusions: The real-time PCR assays were species-specific and sensitive. Singular or multiplex real-time PCR assays could detect target pathogens from both bulked seed samples as well as single spinach seed., Significance and Impact of the Study: The freeze-blotter assay that is currently routinely used in the spinach seed industry to detect and quantify three fungal seedborne pathogens of spinach (C. variabile, S. botryosum and V. dahliae) is quite laborious and takes several weeks to process. The real-time PCR assays developed in this study are more sensitive and can be completed in a single day. As the assays can be applied easily for routine seed inspections, these tools could be very useful to the spinach seed industry., (© 2014 The Society for Applied Microbiology.)

Downy mildew, caused by Peronospora farinosa f. sp. spinaciae (= P. effusa) is an economically important disease in most areas where spinach is grown. This disease has become increasingly important in intensive production fields for pre-packaged salad mixes where plant densities typically are very high (2). However, little is known about race diversity of the downy mildew pathogen of spinach in smaller (<1 ha) production areas. Small (~0.1 ha) spinach production fields in Fayoum, Egypt, often intercropped with lettuce, were examined in February 2013. Downy mildew was observed in three spinach fields in the Fayoum area. Most of the cultivars being grown were traditional cultivars commonly grown from locally produced open pollinated seed. Disease incidence was relatively low with only about 10% of the plants showing symptoms of infection. Symptoms of downy mildew were observed on the cultivar Meky, and included chlorotic spots with blue-gray sporulation on the underside of the symptomatic leaves. Microscopic examination revealed sporangia, measuring 20.2 × 30.5 μm, and monopodial sporangiaphores of 180 to 330 μm length matching the description of P. farinosa f. sp. spinaciae (1). In addition, the pathogen was identified by examination of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) sequence, which had 100% identity to a 762-bp ITS sequence in GenBank of P. farinosa f. sp. spinaciae (Accession No. DQ643879.1). The Fayoum area of Egypt gets relatively low annual rainfall, typically <10 to 15 cm annually, often concentrated in the winter months of November to February, followed by very hot, dry summer months. Although downy mildew of spinach has been reported in Israel, adjacent to Egypt, the disease apparently is relatively rare in the arid Middle East (3). This is the first known report of downy mildew of spinach in Egypt. References: (1) Y. Choi et al. Mycol. Res. 111:318, 2007. (2) J. C. Correll et al. Eur. J. Plant Pathol. 2011. (3) T. Rayss. Palest. J. Bot. Jerusalem Ser. 1:313, 1938.

Spinach downy mildew disease, caused by the obligate pathogen Peronospora farinosa f. sp. spinaciae, is the most economically important spinach (Spinacia oleracea) disease. New races of this pathogen have been emerging at a rapid rate over the last 15 years. This is likely due to production changes, particularly in California, such as high-density plantings and year-round spinach production. As of 2004, 10 races of P. farinosa f. sp. spinaciae had been identified, and the spinach resistance locus RPF2 provided resistance to races 1 to 10. Based on disease reactions on a set of spinach differentials containing six hypothesized resistance loci (RPF1-RPF6), races 11, 12, 13, and 14 of P. farinosa f. sp. spinaciae were characterized based on samples collected in the past 5 years as part of this study. Race 11, identified in 2008, could overcome the resistance of spinach cultivars resistant to races 1 to 10. Spinach resistance loci RPF1, RPF3, and RPF6 provided resistance to race 11. Race 12 was identified in 2009 and could overcome the resistances of the RPF1 and RPF2 loci. The RPF3 locus was effective against race 12. Race 13 was identified in 2010 and could overcome the resistance imparted by the RPF2 and RPF3 loci, whereas the RPF1 locus was effective against race 13. Race 14 was similar to race 12 and caused identical disease responses on the standard differentials but could be distinguished from race 12 by its ability to cause disease on a number of newly released cultivars, including 'Pigeon', 'Cello', and 'Celesta'. Five novel strains of P. farinosa f. sp. spinaciae were also identified. For example, isolate UA4711 of the pathogen, collected from Spain in 2011, was able to overcome the resistance imparted by the RPF1 and RPF3 loci, while RPF2 and RPF4 were effective against this strain. A total of 116 spinach cultivars, including 103 commercial lines and 13 differential cultivars, were evaluated for resistance to race 10 and the newly designated races 11, 12, 13, and 14.

In 2005, Verticillium dahliae was first reported to be pathogenic to spinach seed crops in the Pacific Northwest, with symptoms only developing after initiation of the reproductive stage of plant growth, and to be prevalent on commercial spinach seed lots produced in Denmark, The Netherlands, and the United States. In this study, the genetic diversity, pathogenicity, and virulence were examined for a collection of isolates of Verticillium spp. from spinach as well as other hosts (alfalfa, cotton, lettuce, mint, peppermint, potato, radish, and tomato) from various countries and from different vegetative compatibility groups (VCGs). Of a total of 210 isolates of V. dahliae obtained from spinach seed produced in Denmark, the Netherlands, New Zealand, or the United States, 128 were assigned to VCG 4B (89% of 91 U.S. isolates, 86% of 42 isolates from the Netherlands, 19% of 43 Denmark isolates, and 8% of 13 New Zealand isolates), 65 to VCG 2B (92% of the New Zealand isolates, 79% of the Denmark isolates, 14% of the Netherlands isolates, and 9% of the U.S. isolates), and 3 to VCG 2A (2% of each of the Denmark and U.S. isolates, and 0% of the Netherlands and New Zealand isolates); 14 isolates could not be assigned to a VCG. Although little variation in the sequence of the internal transcribed spacer (ITS) region of ribosomal DNA was observed among isolates within each Verticillium sp., the ITS region readily differentiated isolates of the species V. dahliae, V. tricorpus, and Gibellulopsis nigrescens (formerly V. nigrescens) obtained from spinach seed. Greenhouse pathogenicity assays on spinach, cotton, lettuce, and tomato plants using isolates of V. dahliae (n = 29 to 34 isolates), V. tricorpus (n = 3), G. nigrescens (n = 2), and V. albo-atrum (n = 1) originally obtained from these hosts as well as from alfalfa, mint, peppermint, potato, and radish, revealed a wide range in virulence among the isolates. Isolates of V. tricorpus and G. nigrescens recovered from spinach seed and an isolate of V. albo-atrum from alfalfa were not pathogenic on spinach. In addition, isolates of V. dahliae from mint and peppermint were not pathogenic or only weakly virulent on the hosts evaluated. Although there was a wide range in virulence among the isolates of V. dahliae tested, all of the V. dahliae isolates caused Verticillium wilt symptoms on spinach, lettuce, tomato, and cotton. None of the isolates of V. dahliae showed host specificity. These results indicate that Verticillium and related species associated with spinach seed display substantial variability in virulence and pathogenicity to spinach and other plants but the V. dahliae isolates were restricted to three VCGs.

Background: In recent years, a disease caused by Southern rice black-streaked dwarf virus (SRBSDV) has resulted in significant loss in rice production in Southern China and has spread quickly throughout East and Southeast Asia. This virus is transmitted by an insect vector, white-backed planthopper (WBPH) Sogatella furcifera (Hemiptera: Delphacidae), in a persistent propagative manner. Aside from rice, SRBSDV can also infect numerous Poaceae plants. However, the molecular mechanism of interaction between SRBSDV and its plant or insect vector remains unclear. In order to address this, we investigated the whole viral genome relative mRNA expression level in distinct hosts and monitored their expression level in real-time in rice plants., Methods: In this study, a reliable, rapid, and sensitive method for detecting viral gene expression transcripts is reported. A SYBR Green I based real-time polymerase chain reaction (PCR) method was adopted for the quantitative detection of SRBSDV gene expression in different hosts and real-time changes in gene expression in rice., Results: Compared to the relative mRNA expression level of the whole genome of SRBSDV, P3, P7-1, and P9-2 were dominantly expressed in rice and WBPH. Similarly, these genes also exhibited high expression levels in corn, suggesting that they have more important functions than other viral genes in the interaction between SRBSDV and hosts, and that they could be used as molecular detection target genes of SRBSDV. In contrast, the levels of P6 and P10 were relative low. Western blotting analysis partially was also verified our qPCR results at the level of protein expression. Analysis of the real-time changes in SRBSDV-infected rice plants revealed four distinct temporal expression patterns of the thirteen genes. Moreover, expression levels of P1 and other genes were significantly down-regulated on days 14 and 20, respectively., Conclusion: SRBSDV genes showed similar expression patterns in distinct hosts (rice, corn, and WBPH), indicating that SRBSDV uses the same infection strategy in plant and insect hosts. P3, P7-1, and P9-2 were the dominantly expressed genes in the three tested hosts. Therefore, they are likely to be genes with the most crucial function and could be used as sensitive molecular detection targets for SRBSDV. Furthermore, real-time changes in SRBSDV genes provided a basis for understanding the mechanism of interaction between SRBSDV and its hosts.

The Pi-ta gene deployed in southern U.S. rice germplasm is effective in preventing the infection by strains of Magnaporthe oryzae isolates that carry the avirulence (AVR) gene AVR-Pita1. In the present study, 169 isolates from rice (Oryza sativa) cultivars, with and without Pi-ta, were analyzed for their genetic identity using an international differential system, repetitive element-based polymerase chain reaction (Rep-PCR), and sequence analysis of PCR products of AVR-Pita1. These isolates belong to the races IA1, IB1, IB17, IC1, and IC17 of M. oryzae. These isolates were further classified into 15 distinct groups by Rep-PCR. There was a predominant group within each race. Pathogenicity assays on 'Katy' (Pi-ta) and 'M202' (pi-ta) rice determined that IC1 was virulent to Katy and M202; IB17, IC17, and most of IA1 and IB1 were avirulent to Katy and virulent to M202, suggesting that the Pi-ta gene in Katy is responsible for preventing infection by these isolates. Consistently, AVR-Pita1 was not amplified from 28 virulent isolates. One AVR-Pita1 allele was amplified by AVR-Pita1-specific primers in 78 avirulent isolates. Interestingly, different AVR-Pita1 alleles were found in each of the 12 avirulent isolates, as determined by DNA sequencing. Sequence analysis of 90 PCR products revealed 10 AVR-Pita1 haplotypes, 4 of which were new. In total, 12 amino acid changes were identified in the new variants when compared with the first described AVR-Pita sequence (AF207841). The finding of isolates with altered AVR-Pita1 from rice cultivars with and without Pi-ta suggests that these virulent isolates were adapted to the field environments in the southern United States. Further research will be needed to verify this prediction.

Rice sheath blight disease, caused by Rhizoctonia solani AG1-1A, is one of the most destructive rice diseases worldwide. Utilization of host resistance is the most economical and environmentally sound strategy in managing sheath blight (ShB). Ten ShB quantitative trait loci (QTLs) were previously mapped in a Lemont × Jasmine 85 recombinant inbred line (LJRIL) population using greenhouse inoculation methods at an early vegetative stage. However, confirmation of ShB-resistant QTLs under field conditions is critical for their utilization in marker-assisted selection (MAS) for improving ShB resistance in new cultivars. In the present study, we evaluated ShB resistance using 216 LJRILs under field conditions in Arkansas, Texas, and Louisiana during 2008 and 2009. We confirmed the presence of the major ShB-QTL qShB9-2 based on the field data and also identified one new ShB-QTL between markers RM221 and RM112 on chromosome 2 across all three locations. Based on the field verification of ShB evaluations, the microchamber and mist-chamber assays were simple, effective, and reliable methods to identify major ShB-QTLs like qShB9-2 in the greenhouse at early vegetative stages. The markers RM215 and RM245 were found to be closely linked to qShB9-2 in greenhouse and field assays, indicating that they will be useful for improving ShB resistance in rice breeding programs using MAS.

Following prolonged spring rains and cool summer weather in 2010, mature weeping willow trees (Salix babylonica L.) growing next to a manmade lake in Marin County, CA, showed symptoms of a previously undescribed disease. During summer, small branches developed dark brown to black, sunken cankers. Canker lengths ranged from 3 to 20 cm. Within the cankered areas, affected twigs, shoots, and leaves turned brown, collapsed, and died. The distal portions of infected branches also died, giving the trees a blighted appearance. Acervuli and pink sporulation were observed in the canker tissue. When placed on acidified potato dextrose agar (A-PDA), canker tissues consistently yielded one type of fungal organism. On A-PDA, isolates produced gray aerial mycelium, acervuli, and single-celled fusiform conidia. Two isolates were identified as Colletotrichum acutatum based on sequence analysis of the ITS region of the ribosomal DNA and the 1-kb intron of the glutamine synthase gene (1) and fungal morphology (2,3) (GenBank Accession Nos. JQ951597 and JQ951598). The willow isolates examined were identified as C. acutatum based on a 99% identity of the ITS sequence with accession FR716517 and a 98% identity of the 1-kb intron sequence with accession GQ387248 in GenBank. Interestingly, the isolates were confirmed to be homothallic producing perithecia from monoconidial cultures. To demonstrate Koch's postulates, inocula were prepared from 2-week-old colonies of each of four isolates grown on A-PDA. Using containerized weeping willow trees as test material, shallow slits were cut into the epidermis of small (1.5-cm diameter or less) branches; one colonized agar plug was placed within each cut area and the epidermis was resealed by wrapping the branch with Parafilm. Ten inoculations were made for each isolate and inoculated plants were maintained in a greenhouse. After 4 weeks, inoculated branches exhibited dark cankers and twig dieback. C. acutatum was reisolated from all symptomatic cankers and matched the characteristics of the original isolates. Control twigs, inoculated with sterile agar plugs, did not develop any blight symptoms. This experiment was repeated and the results were the same. To our knowledge, this is the first documentation of C. acutatum as a pathogen of weeping willow in California. The disease resulted in repeated defoliation of trees in the Santa Venetia area of Marin County. Badly infected trees declined as a result of repeated defoliation and twig loss. Discussions with parks personnel suggested that the disease may have been present at low levels in the area for some years, and that disease severity increased dramatically with weather that was atypically wet and cool (max. mean temps. 5.5°C cooler and 6 cm more total rainfall than the records of the previous two years) for the area during May and June 2010, when the disease was discovered. References: (1) J. C. Guerber et al. Mycologia 95:872, 2003. (2) P. S. Gunnell and W. D. Gubler. Mycologia 84:157, 1992. (3) B. J. Smith and L. L. Black. Plant Dis. 74:69, 1990.

In September 2010, celery plants with leaf cupping and petiole twisting were observed in commercial production fields located in Barry, Kent, Newago, and Van Buren Counties in Michigan. Long, elliptical lesions were observed on petioles but signs (mycelia, conidia, or acervuli) were not readily observed. Celery petioles were incubated in humid chambers (acrylic boxes with wet paper towels). After 24 h, conidia corresponding to the genus Colletotrichum were observed. Isolations were performed by excising pieces of celery tissue from the lesion margin and placing them on potato dextrose agar (PDA) amended with 30 ppm of rifampicin and 100 ppm of ampicillin. Plates were incubated at 21 ± 2°C under fluorescent light for 5 days. Fungal colony morphology was gray with salmon-colored masses of spores when viewed from above, and carmine when viewed from below. Isolates were single-spored and placed on 30% glycerol in -20°C, and cryoconservation media (20% glycerol, 0.04% yeast extract, 0.1% malt extract, 0.04% glucose, 0.02% K 2 HPO 4 ) at -80°C. Conidia were 8.5 to 12.0 × 2.8 to 4.0 μm and straight fusiform in shape. Three isolates were confirmed as C. acutatum sensu lato based on sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA and the 1-kb intron of the glutamine synthase gene (3), both with 100% similarity with Glomerella acutata sequences. Sequences were submitted to GenBank (Accession Nos. JQ951599 and JQ951600 for ITS and GS, respectively). Additionally, C. acutatum specific primer CaIntg was used in combination with the primer ITS4 on 54 isolates from symptomatic celery plants, obtaining the expected 490-pb fragment (1). Koch's postulates were completed by inoculating 4-week-old celery seedlings of cultivars Sabroso, Green Bay, and Dutchess using three plants per cultivar. Prior to inoculation, seedlings were incubated for 16 h in high relative humidity (≥95%) by enclosing the plants in humid chambers. Seven-day-old C. acutatum s. l. colonies were used to prepare the inoculum. Seedlings were spray-inoculated with a C. acutatum s. l. conidial suspension of 1 × 10 6 conidia/ml in double-distilled water plus Tween 0.01%. Two control seedlings per cultivar were sprayed with sterile, double-distilled water plus 0.01% Tween. Plants were enclosed in bags for 96 h post inoculation and incubated in a greenhouse at 27°C by day/20°C by night with a 16-h photoperiod. Leaf curling was observed on all inoculated plants of the three cultivars 4 days after inoculation (DAI). Petiole lesions were observed 14 to 21 DAI. Conidia were observed in lesions after incubation in high humidity at 21 ± 2°C for 24 to 72 h. Symptomatic tissue was excised and cultured onto PDA and resulted in C. acutatum colonies. Control plants remained symptomless. C. acutatum (4) and C. orbiculare (2) were reported to cause celery leaf curl in Australia in 1966 (2,4). To our knowledge, this is the first report of C. acutatum s. l. infecting celery in Michigan. References: (1) A. E. Brown et al. Phytopathology 86:523, 1996. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab., USDA-ARS. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , 10 September 2010. (3) J. C. Guerber et al. Mycologia 95:872, 2003. (4) D. G. Wright and J. B. Heaton. Austral. Plant Pathol. 20:155, 1991.

We used qualitative methods (13 homogenous focus groups of residents, bereaved family members, licensed staff, paraprofessional staff, and social workers) to examine the components of a good death in a long-term care (LTC). Hospice involvement as beneficial to end-of-life care emerged as a naturally occurring theme and hospice was deemed as expert in all groups. Participants indicated some barriers to hospice involvement as well as difficulties in collaboration between facility staff and hospice personnel. When viewed within the context of existing literature, these data suggest that a new model of hospice care in which hospice staff serve as expert consultants may be appropriate. This model that recognizes and optimizes the experience of both the facility staff and hospice personnel will benefit care recipients.

In July of 2010, dry, oval lesions, each with a salmon-colored center and bleached overall appearance, were observed on the leaves and neck of onions plants growing in production fields of Newaygo, Ottawa, Kent, and Ionia counties, Michigan. Acervuli and setae that are characteristic of Colletotrichum spp. were observed with a dissecting microscope, and elliptical conidia (8 to 23 × 3 to 12 μm) with attenuated ends were observed with a compound microscope. Symptomatic tissues were excised and cultured onto potato dextrose agar amended with 30 and 100 ppm of rifampicin and ampicillin, respectively. The cultures produced pale salmon-colored sporulation after growing for 5 days at 22 ± 2°C and black microsclerotia after 2 weeks. Six isolates were confirmed as C. coccodes based on sequence analysis of the internal transcribed (ITS) region of the ribosomal DNA and a 1-kb intron of the glutamine synthase gene (GS) (2). Sequences were submitted to GenBank (Accession Nos. JQ682644 and JQ682645 for ITS and GS, respectively). Pathogenicity tests were conducted on two- to three-leaved 'Stanley' and 'Cortland' onion seedlings. Prior to inoculation, seedlings were enclosed in clear plastic bags overnight to provide high relative humidity. The bags were removed, and seedlings were sprayed inoculated with a C. coccodes conidial suspension (5 × 10 5 conidia/ml and 25 ml/plant) in sterile double-distilled water. Control seedlings were sprayed with sterile double-distilled water. Tween (0.01%) was added to the conidial suspension and the water. Plants were enclosed in bags for 72 h postinoculation and incubated in growth chambers at 28°C day/23°C night with a 12-h photoperiod. Sunken, oval lesions were observed on the foliage of the onion seedlings inoculated with C. coccodes 4 days postinoculation. Lesions coalesced and foliage collapsed 7 days postinoculation. Control plants remained asymptomatic. When five leaf samples per replication were detached and incubated in a moist chamber for 3 days at 21 ± 2°C, abundant acervuli and setae were observed on the symptomatic tissue but not on control tissue. C. coccodes was consistently recovered from the onion seedling lesions. Six different Colletotrichum spp. have been reported to cause diseases on onions worldwide (1,4). C. circinans, which causes smudge, is an occasional onion pathogen in Michigan, while C. gloeosporioides has only been reported to be infecting onions in Georgia (3). To our knowledge, this is the first report of C. coccodes infecting and causing disease in onions plants. References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , August 6, 2010. (2) J. C. Guerber et al. Mycologia 95:872. 2003. (3) C. Nischwitz et al. Plant Dis. 92:974. 2008. (4) H. F. Schwartz, and K. S. Mohan. Compendium of Onion and Garlic Diseases and Pests, 2nd ed. The American Phytopathological Society, St. Paul, MN. 1995.

In California, perennial pepperweed (Lepidium latifolium) is an introduced Brassicaceae plant that is invasive, highly competitive, and listed as a noxious weed that grows in areas such as marshes, meadows, roadsides, and irrigation ditches. From 2008 through 2010, perennial pepperweed growing near farms in Monterey and Santa Clara counties was infected with white rust. Symptoms were light green-to-chlorotic spots on adaxial leaf surfaces and corresponding white, blister-like sori growing underneath the raised leaf epidermis on the abaxial surface. Sporangia were collected from lesions and used for DNA extraction. The internal transcribed spacer (ITS) region was amplified with primers ITS1/ITS4 and sequenced. The sequence matched with Albugo candida by BLAST against GenBank. On the basis of morphological and molecular data, the pathogen was confirmed to be A. candida. Pathogenicity was tested by scraping sporangia from infected leaves and spraying a suspension (1 × 10 5 sporangia/ml) onto pepperweed seedlings grown in pots. Plants were placed in an incubator at 100% relative humidity and 12°C for 48 h to induce zoospore release. Plants were subsequently maintained in a greenhouse. After 15 to 17 days, inoculated plants developed white rust symptoms and signs. Control plants sprayed with water did not become diseased. The experiment was completed two times with the same results. To determine the race of A. candida from perennial pepperweed, 4- to 5-week-old plants and 1- to 2-week-old seedlings of differential hosts (1-4) were inoculated in a similar fashion. The differential hosts were the following: Raphanus sativus (race 1), Brassica juncea cv. Burgonde (race 2A), B. juncea cv. Cutlass (race 2V), Armoracia rusticana (race 3), Capsella bursa-pastoris (race 4), Sisymbrium officinale (race 5), Rorippa islandica (race 6), B. rapa (B. campestris) cv. Torch (race 7A), B. rapa cvs. Reward, Cutlass, and AC Parkland (race 7V), B. nigra (race 8), B. oleracea (race 9), Sinapis alba (race 10), B. carinata (race 11), and perennial pepperweed as a control. White rust developed on pepperweed 10 to 14 days later but was not found on any of the differential hosts, indicating that this pathogen is not one of the currently described 11 races. The following commercial crop species were inoculated using the same method: arugula (Eruca sativa), Japanese mustard (B. campestris subsp. nipposinica), red mustard (B. juncea subsp. rugosa), tah tsai (B. campestris subsp. narinosa), cauliflower (B. oleracea subsp. botrytis), Chinese cabbage (B. campestris subsp. pekinensis), bok choy (B. rapa Chinensis group), broccoli raab (B. rapa subsp. rapa), and perennial pepperweed as a control. Only the perennial pepperweed developed white rust. To our knowledge, this is the first characterization of A. candida infecting perennial pepperweed in California. The disease has been documented on this plant in Colorado and also in Bulgaria, Portugal, and Spain. The host range information is important to growers because it indicates that the race currently infecting perennial pepperweed will not infect commercial crucifers. References: (1) P. A. Delwich and P. H. Williams. Cruciferae Newsl. 2:39, 1977. (2) C. B. Hill et al. Cruciferae Newsl. 13:112, 1988. (3) S. R. Rimmer et al. Can. J. Plant Pathol. 22:229, 2000. (4) P. R. Verma et al. Can. J. Bot. 53:1016, 1975.

In California, sunflower (Helianthus annuus) is commercially grown and marketed as edible, germinated sprouts. Sunflower seeds are soaked overnight in water, drained, and seeded into a compost-based medium in flats. The flats are incubated for 3 days in low-light conditions until roots develop. Flats are then moved under filtered shade, with air circulation provided by fans, for 3 to 5 days. The germinated seedlings are finally grown in full sunlight for another 3 to 7 days and are then ready for market. Such sprouts can be consumed raw or cooked. In 2009, in Placer County, CA, a previously undescribed disease occurred on commercial organic sunflower sprouts. Symptoms were dark brown, irregularly shaped lesions on seedling cotyledons and stems. Fungal fruiting structures were not observed in diseased tissues. Isolations were carried out on symptomatic seedlings that were surface sanitized in 1.2% NaOCl and then rinsed in sterile distilled water (SDW). When placed on acidified potato dextrose agar (A-PDA), tissues consistently yielded one type of fungal organism. On A-PDA, isolates produced dark gray, aerial mycelium, acervuli, and single-celled fusiform conidia. Eight isolates were examined for sequence variation in the internal transcribed spacer (ITS) region and the intron in the glutamine synthetase (GS) gene (2). On the basis of spore morphology and a complete match (100%) of the ITS sequence and the GS intron sequence, all eight isolates were identified as Colletotrichum acutatum subgroup C1 represented by isolate ATCC MYA-662 (2). Six isolates were each tested for pathogenicity on sunflower by spraying a spore suspension (1 × 10 6 conidia/ml) onto sets (six-pack trays; one plant per cell) of plants at either cotyledon or first true-leaf stage. Each plant set was sprayed with approximately 5 to 8 ml of inoculum. Plants were incubated for 48 h in a humidity chamber and then maintained in a greenhouse. Control sunflower plants were sprayed with distilled water and otherwise treated similarly. After 14 days, inoculated cotyledons and true leaves developed lesions similar to those observed on commercial samples; C. acutatum was reisolated from these lesions. Control plants developed no symptoms. The experiment was repeated and the results were the same. To test for possible seedborne C. acutatum, sunflower seeds of the same commercial seed lot used to plant the affected crop were surface sanitized (1.2 % NaOCl for 60 s), rinsed in SDW, placed in incubation boxes (10.2 × 10.2 cm, clear acrylic, Hoffman Manufacturing, Inc., Jefferson, OR), and then processed according to a previously described freeze blotter assay (1). After testing 10 replications of 100 seeds each, no C. acutatum was detected. To our knowledge, this is the first report of anthracnose of sunflower sprouts in California and the first report of a sunflower disease caused by C. acutatum. This sprout production environment, consisting of high humidity, prolonged periods of high moisture, and low light, likely favored the disease. For the affected commercial sprouts crops, disease reached as high as 25% incidence and continues to be an intermittent problem. References: (1) L. J. du Toit et al. Plant Dis. 89:4, 2005. (2) J. C. Guerber et al. Mycologia 95:872, 2003.

Rice sheath blight (ShB), caused by the soilborne pathogen Rhizoctonia solani, annually causes severe losses in yield and quality in many rice production areas worldwide. Jasmine 85 is an indica cultivar that has proven to have a high level of resistance to this pathogen. The objective of this study was to determine the ability of controlled environment inoculation assays to detect ShB resistance quantitative trait loci (QTLs) in a cross derived from the susceptible cv. Lemont and the resistant cv. Jasmine 85. The disease reactions of 250 F(5) recombinant inbred lines (RILs) were measured on the seedlings inoculated using microchamber and mist-chamber assays under greenhouse conditions. In total, 10 ShB-QTLs were identified on chromosomes 1, 2, 3, 5, 6, and 9 using these two methods. The microchamber method identified four of five new ShB-QTLs, one on each of chromosomes 1, 3, 5, and 6. Both microchamber and mist-chamber methods identified two ShB-QTLs, qShB1 and qShB9-2. Four of the ShB-QTLs or ShB-QTL regions identified on chromosomes 2, 3, and 9 were previously reported in the literature. The major ShB-QTL qShB9-2, which cosegregated with simple sequence repeat (SSR) marker RM245 on chromosome 9, contributed to 24.3 and 27.2% of total phenotypic variation in ShB using microchamber and mistchamber assays, respectively. qShB9-2, a plant-stage-independent QTL, was also verified in nine haplotypes of 10 resistant Lemont/Jasmine 85 RILs using haplotype analysis. These results suggest that multiple ShB-QTLs are involved in ShB resistance and that microchamber and mist-chamber methods are effective for detecting plant-stage-independent QTLs. Furthermore, two SSR markers, RM215 and RM245, are robust markers and can be used in marker-assisted breeding programs to improve ShB resistance.

During 2008, fruit rot of pumpkin (Cucurbita pepo L.) occurred on several cultivars in commercial fields in northeast and northwest Arkansas. Disease incidence ranged from 50 to 75% of the fruit, which were unmarketable. Symptoms included large (>10 cm), brown, corky lesions where the fruit was in contact with the soil. Initially, the lesions were water soaked. A cross section of the symptomatic fruit rind revealed a dry, brown, spongy rot with a light brown halo. Lesions finally became soft and wet, causing infected fruit to collapse. Masses of white mycelia surrounded advanced lesions. No rot symptoms were observed on the vines. Fusarium spp. were isolated from symptomatic fruit. Macroconidia obtained from field-infected fruit and pure potato dextrose agar (PDA) cultures of the predominant Fusarium sp. were morphologically similar. The straight, cylindrical, and robust macroconidia contained between five and seven septa. The apical cell was rounded and blunt and the basal cell was rounded. All three morphological types were tested for pathogenicity on mature fruit of cv. Sorcerer. Fruit were surface disinfected in 70% ethanol. Wounds were made (4 mm deep) in the fruit surface with a cork borer. Three wounds per isolate per fruit were inoculated with a PDA plug colonized with mycelium from a 3-day-old culture. Three replicated wounds were inoculated per isolate and four replicate fruit were used. After inoculation, the wounds were covered with saran wrap. The fruit were incubated at approximately 24°C and evaluated after 7 days. An uncolonized PDA plug was used as a negative control. After 7 days, only the predominant Fusarium sp. produced typical lesions, which were brown, water soaked, and approximately 3 cm in diameter. Fusarium spp. were recovered from the inoculated lesions. The colonies on PDA and macroconidia of the pathogenic Fusarium sp. were morphologically similar to the isolate inoculated and the ones recovered from field lesions. DNA was extracted from the same three isolates used in the pathogenicity test. A portion of the translation elongation factor 1α (TEF) gene was sequenced to verify the identity of the pathogenic isolates. On the basis of a comparison of the Fusarium-ID database at Pennsylvania State University (3), the pathogenic isolates had a 100% match with Fusarium solani f. sp. cucurbitae race 1, teleomorph Nectria haematococca mating population I, isolate NRRL 22098. F. solani f. sp cucurbitae was previously identified as the causal agent of crown and foot rot and a fruit rot of cucurbits and responsible for outbreaks on pumpkin fruit in Connecticut, Missouri, New York, and Ohio from 2001 to 2003 and again in Ohio in 2005 (2). In 2008, a higher average total of monthly precipitation was recorded late in the growing season in Arkansas, (13.7 cm in August and 23.7 cm in September). Although F. equiseti has previously been reported as a fruit rot pathogen of pumpkin in Arkansas (1), to our knowledge, this is the first report of F. solani f. sp cucurbitae as causal agent of pumpkin fruit rot in the state. Reference: (1) J. C. Correll et al. Plant Dis. 75:751, 1991. (2) W. H. Elmer et al. Plant Dis. 91:1142, 2007. (3) D. M. Geiser et al. Eur. J. Plant Pathol. 110:473, 2004.

Downy mildew is a destructive disease of spinach worldwide. There have been 10 races described since 1824, six of which have been identified in the past 10 years. Race identification is based on qualitative disease reactions on a set of diverse host differentials which include open-pollinated cultivars, contemporary hybrid cultivars, and older hybrid cultivars that are no longer produced. The development of a set of near-isogenic open-pollinated spinach lines (NILs), having different resistance loci in a susceptible and otherwise common genetic background, would facilitate identification of races of the downy mildew pathogen, provide a tool to better understand the genetics of resistance, and expedite the development of molecular markers linked to these disease resistance loci. To achieve this objective, the spinach cv. Viroflay, susceptible to race 6 of Peronospora farinosa f. sp. spinaciae, was used as the recurrent susceptible parent in crosses with the hybrid spinach cv. Lion, resistant to race 6. Resistant F(1) progeny were subsequently backcrossed to Viroflay four times with selection for race 6 resistance each time. Analysis of the segregation data showed that resistance was controlled by a single dominant gene, and the resistance locus was designated Pfs-1. By bulk segregant analysis, an amplified fragment length polymorphism (AFLP) marker (E-ACT/M-CTG) linked to Pfs-1 was identified and used to develop a co-dominant Sequence characterized amplified region (SCAR) marker. This SCAR marker, designated Dm-1, was closely linked ( approximately 1.7 cM) to the Pfs-1 locus and could discriminate among spinach genotypes that were homozygous resistant (Pfs-1Pfs-1), heterozygous resistant (Pfs-1pfs-1), or homozygous susceptible (pfs-1pfs-1) to race 6 within the original mapping population. Evaluation of a wide range of commercial spinach lines outside of the mapping population indicated that Dm-1 could effectively identify Pfs-1 resistant genotypes; the Dm-1 marker correctly predicted the disease resistance phenotype in 120 out of 123 lines tested. In addition, the NIL containing the Pfs-1 locus (Pfs-1Pfs-1) was resistant to multiple races of the downy mildew pathogen indicating Pfs-1 locus may contain a cluster of resistance genes.

Cultivation of brassica vegetables has the highest potential for generating income among more traditional rice and maize farmers in Nepal. Among brassica vegetables, the most important are cauliflower (Brassica oleracea var. botrytis L.) and cabbage (B. oleracea var. capitata L.). Although clubroot disease, caused by Plasmodiophora brassicae Woronin, has been observed in Nepal since 1993, severe and widespread epidemics have been observed since 2004 in the Bhaktapur, Kathmandu, Lalitpur, and Palung Valley production areas. Typical disease symptoms (1) are widespread, and disease severity has been particularly severe in the Kathmandu Valley and Palung/Daman area of the Makwanpur District. Many cauliflower fields in these areas have had as much as 100% yield loss between 2004 and 2006 with an estimated 40% overall loss from clubroot. Estimates from interviews with growers in the Palung production area during an intensive farmers' interaction program indicated that cauliflower production was reduced from 5 to 6 metric tons per household (1,500 m 2 ) prior to 2004 to <300 kg per household in 2004 and beyond. The economic loss in this area alone was estimated at $1.4 million in 2004 and 2005. Examination of transplant nurseries indicated that frequently >80% of the seedlings have symptoms of clubroot at the time of transplanting. Soil samples from throughout the production areas indicated that the sandy loam soils were predominately acidic (pH range of 4.2 to 7.2 with >90% below 6.0). Several management practices are being employed to reduce disease severity, including the use of clubroot resistant cultivars, raising the soil pH to >7.0 by using dolomitic lime, testing of the fungicide flusulfamide (Nebijin) and biopesticide Sanjeevani (Trichoderma viride), and biofumigation and solarization of the nursery beds in an effort to reduce disease pressure on transplant material. References: (1) G. R. Dixon. Compendium of Brassica Diseases. S. R. Rimmer et al., eds. American Phytopathological Society, St. Paul, 2007.

Spinach downy mildew, caused by Peronospora farinosa f. sp. spinaciae, is the most economically important disease of spinach worldwide. During the past few years, spinach cultivars resistant to the seven previously described races of P. farinosa f. sp. spinaciae were observed to be severely affected by downy mildew in both the United States and the European Union. Four new isolates of P. farinosa f. sp. spinaciae were collected from California and The Netherlands and characterized based on disease reactions on two modified sets of spinach differentials. The results led to the description of three new races of the downy mildew pathogen, designated races 8, 9, and 10. Four differential cultivars with resistance to races 1 to 7 were used to distinguish the three new races. Dolphin was susceptible to races 8 and 10 but resistant to race 9; Lion was susceptible to race 10 but resistant to races 8 and 9; Lazio was resistant to races 1 to 7 as well as races 8, 9, and 10; and Tarpy was susceptible to all three new races. The three new races also were used to evaluate the disease reactions on 43 contemporary commercial spinach cultivars in greenhouse trials. A survey of 58 isolates of P. farinosa f. sp. spinaciae collected in California and Arizona between 2004 and 2006 revealed that race 10 predominated in the areas sampled.

The avirulence gene AVR-Pita of Magnaporthe oryzae determines the efficacy of the resistance gene Pi-ta in rice. The structures of the AVR-Pita alleles in 39 US isolates of M. oryzae were analyzed using polymerase chain reaction. A series of allele-specific primers were developed from the AVR-Pita gene to examine the presence of AVR-Pita. Orthologous alleles of the AVR-Pita gene were amplified from avirulent isolates. Sequence analysis of five alleles revealed three introns at identical positions in the AVR-Pita gene. All five alleles were predicted to encode metalloprotease proteins highly similar to the AVR-Pita protein. In contrast, the same regions of the AVR-Pita alleles were not amplified in the most virulent isolates, and significant variations of DNA sequence at the AVR-Pita allele were verified by Southern blot analysis. A Pot3 transposon was identified in the DNA region encoding the putative protease motif of the AVR-Pita protein from a field isolate B2 collected from a Pi-ta-containing cultivar Banks. These findings show that transposons can contribute to instability of AVR-Pita and is one molecular mechanism for defeating resistance genes in rice cultivar Banks.

ABSTRACT Based on spore morphology, appressorium development, sequence similarities of the rDNA, and similarities in amplified restriction fragment length polymorphism (AFLP), it has been proposed that Colletotrichum orbiculare, C. trifolii, C. lindemuthianum, and C. malvarum represent a single phylogenetic species, C. orbiculare. In the current study, the phylogenetic relationship among isolates in the C. orbiculare species complex was reassessed. In all, 72 isolates of C. orbiculare from cultivated cucurbit or weed hosts, C. trifolii from alfalfa, C. lindemuthianum from green bean, and C. malvarum from prickly sida (Sida spinosa) were examined for mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs), RFLPs and sequence variation of a 900-bp intron of the glutamine synthetase gene and a 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase gene, and vegetative compatibility. In addition, host specificity was examined in foliar inoculations on cucurbit, bean, and alfalfa hosts. Inoculations also were conducted on cucumber fruit. Genetically distinct isolates, based on vegetative compatibility, within the species complex (C. orbiculare, C. trifolii, and C. malvarum) had an identical mtDNA haplotype (haplotype A) when examined with each of three different restriction enzymes. Isolates of C. lindemuthianum had a very similar mtDNA haplotype to haplotype A, with a single polymorphism detected with the enzyme HaeIII. The four species represent a phylogenetically closely related group based on a statistical analysis of the 900- and 200-bp intron sequences. However, distinct RFLPs in the 900-bp intron were consistently associated with each species and could be used to qualitatively and quantitatively distinguish each species. Furthermore, each of the species showed distinct host specificity, with isolates of C. orbiculare (from cucurbits), C. lindemuthianum, and C. trifolii being pathogenic only on cucurbits, green bean, and alfalfa, respectively. Consequently, distinct and fixed nucleotide, or genotypic (intron sequences and RFLPs) and phenotypic (host specificity) characteristics can be used to distinguish C. orbiculare, C. lindemuthianum, and C. trifolii from one another; therefore, they should be recognized as distinct species. This species delineation is consistent with the most current species concepts in fungi. More isolates and further characterization is needed to determine whether C. orbiculare from cocklebur and C. malvarum represent distinct species. RFLPs of the 900-bp intron may represent a relatively inexpensive, reliable, and useful diagnostic tool for general species differentiation in the genus Colletotrichum.

Downy mildew, caused by Peronospora farinosa f. sp. spinaciae, is the most economically important disease of spinach (Spinacia oleracea) in the United States and the European Union. In the United States, 23,000 ha of spinach, with a crop value of approximately $170 million, were grown during 2005 (1; http://www.nass.usda.gov/index.asp ). Additionally, per capita, fresh-market spinach consumption has increased 214% in the past decade (1; http://www.nass.usda.gov/index.asp ). Increased demand for fresh-market spinach has led to changes in spinach production practices such as higher planting densities and year-round production. There are currently 10 described races (races 1 to 10) of P. farinosa f. sp. spinaciae. Race 8 was recovered from the Netherlands in 2004 (B. M. Irish, J. Correll, S. T. Koike, and T. Morelock. Plant Dis. [In press]), but has not been previously identified in the United States. In February 2007, several commercial fresh-market spinach fields in central Arizona were severely affected with downy mildew. Symptoms consisted of bright yellow leaf lesions ranging in size from 1 to 3 cm in diameter that supported dense purple sporulation of the pathogen on the corresponding abaxial leaf surface. Affected fields were primarily planted with spinach cv. Parrot, which is reported to be resistant to races 1 to 7 and 9. As much as 32 ha were affected and disease incidence reached as high as 25 to 30%. An isolate (PAR1) of the pathogen was obtained and used to inoculate a standard set of 10 differential spinach cultivars for race identification as previously described (B. M. Irish, J. Correll, S. T. Koike, and T. Morelock. Plant Dis. [In press]). Briefly, a spore suspension (1 × 10 5 sporangia per ml) was misted onto test plants; plants were then incubated in a dew chamber (20°C, 100% relative humidity) for 24 h and maintained in a greenhouse. Inoculation tests were conducted at least twice at each of two different locations (Arkansas and California), with each test including two replications of 15 plants per differential cultivar. The selective development of downy mildew on specific differentials indicated that the isolate was race 8 (B. M. Irish, J. Correll, S. T. Koike, and T. Morelock. Plant Dis. [In press]). To our knowledge, this is the first report of race 8 in the United States. Since there are a number of commercial spinach cultivars available with resistance to race 8, the economic impact of this race in the United States is expected to be low if resistant cultivars are grown (B. M. Irish, J. Correll, S. T. Koike, and T. Morelock. Plant Dis. [In press]). Reference: (1) R. N. Acharya and I. Molina. NFAPP Newsl. Second Quarter, 2005.

Pitahaya, Hylocereus undatus Britt. & Rose, is a columnar, climbing cactus that produces a commercially important fruit. In December 2004, a new disease was found on the crop in Miami-Dade County, FL. Reddish brown lesions with conspicuous chlorotic haloes developed concentrically on the edges of vine ribs. Lesion centers became white and coalesced to rot much of the vine column, and in severe cases, only the vascular column in the vine center was not diseased. Salmon-colored spores and waxy, subepidermal acervuli, typically with setae and simple, short, erect conidiophores, were observed in lesion centers. Tissue from lesion margins was surface disinfested and plated on potato dextrose agar (PDA; Difco Laboratories, Detroit, MI). Colletotrichum gloeosporioides (Penz.) Penz. & Sacc. was isolated from all samples. Colonies produced abundant conidia that were hyaline, one celled, straight, cylindrical, and averaged 14.7 × 5.0 μm with ranges of 12.5 to 17.5 × 3.8 to 7.5 μm (1). Cultural and morphological characteristics of isolates matched those for C. gloeosporioides except for appressoria and hyphopodia (1,2); pitahaya isolates had a spherical rather than lobed hyphopodia reported for C. gloeosporioides and averaged 10.9 (8.5 to 12.7) × 9.1 (7.1 to 10.3) μm. Internal transcribed spacer sequences for the pitahaya isolates were nearly identical (98% homology) to those for C. gloeosporioides isolates occurring on Euphatorium thymifolia in Thailand (GenBank Accession No. AY266393). Koch's postulates were examined in greenhouse trials at the Tropical Research and Education Center, Homestead, FL. Treatments consisted of a noninoculated control, four C. gloeosporioides isolates, and an Alternaria sp. All isolates came from symptomatic pitahaya tissue collected in Miami-Dade County. Fungi were grown on PDA for 7 days at 27°C. A sterile dissecting needle was used to gently pinprick the epidermis of the stem and 2-mm-diameter plugs of C. gloeosporioides, an Alternaria sp., or clean PDA were placed over wounds. Plants were placed in a plastic tent in a greenhouse where the temperature was held at 25°C, and free moisture was maintained on plant surfaces with a household humidifier for 48 h following inoculation. Two isolates of C. gloeosporioides were shown, in repeated greenhouse experiments, to cause reddish brown lesions with conspicuous chlorotic haloes that coalesced to rot much of the vine column, and Koch's postulates were completed with the reisolation of isolates that were used to inoculate plants. The age of vine segments had no significant effect on lesion development. To our knowledge, this is the first report of C. gloeosporioides as a pathogen of pitahaya. References: (1) J. A. Bailey and M. J. Jeger. Colletotrichum: Biology, Pathology and Control. CAB International, Wallingford, UK, 1992. (2) M. Du et al. Mycologia 97:641, 2005.